Contacts of the strand formed by residues 57 - 69 (chain D) in PDB entry 5TIN
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 57 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50D SER 4.4 2.3 - - - +
51D ILE* 3.6 2.6 - - - +
52D ALA* 2.9 34.2 + - - +
55D THR* 2.7 29.0 + - - -
56D MET* 1.3 77.6 - - - +
58D TYR* 1.3 64.9 + - - +
104D LYS* 2.9 35.2 + - + +
135D THR* 3.9 15.9 - - + +
136D LEU 3.1 16.6 - - - +
138D CYS* 3.9 6.7 - - - +
140D MET* 4.5 1.5 - - - +
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Residues in contact with TYR 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D PHE* 3.7 34.8 - + - -
49D GLY 3.9 0.2 - - - +
50D SER 3.6 8.3 - - - -
51D ILE* 3.9 23.6 - - + -
57D ASP* 1.3 75.8 + - - +
59D ARG* 1.3 62.8 + - - +
60D VAL* 3.7 19.7 - - + -
134D LEU 3.7 0.2 - - - +
135D THR* 3.3 7.0 - - - +
136D LEU* 2.8 69.6 + - + +
137D SER 4.3 1.1 - - - -
138D CYS* 3.7 17.9 - - + -
152D CYS* 3.6 22.4 - - + -
153D ILE 2.7 30.6 + - - -
154D MET 4.0 0.7 + - - -
214D PHE* 4.0 10.8 - + - -
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Residues in contact with ARG 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C LYS* 3.6 51.9 + - - +
47D SER* 4.6 1.2 + - - +
48D PHE* 3.5 0.5 - - - -
49D GLY 2.9 40.3 + - - +
50D SER* 3.7 25.5 + - - +
58D TYR* 1.3 76.9 - - - +
60D VAL* 1.3 72.6 + - - +
133D THR* 3.9 27.3 - - + +
134D LEU 3.2 9.4 - - - +
135D THR* 3.9 15.9 - - + +
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Residues in contact with VAL 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D ILE* 4.9 3.1 - - + -
47D SER* 3.3 8.1 - - - +
48D PHE* 3.7 28.0 - - + -
58D TYR* 3.7 16.4 - - + -
59D ARG* 1.3 81.8 - - - +
61D ASN* 1.3 60.9 + - - +
62D ILE* 3.8 22.9 - - + -
132D LEU 3.8 0.3 - - - +
133D THR* 3.3 6.2 - - - +
134D LEU* 2.9 55.0 + - + +
136D LEU* 4.0 13.7 - - + -
154D MET* 4.0 11.0 - - + -
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Residues in contact with ASN 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C GLU 4.9 3.0 + - - +
104C LYS* 6.2 0.4 - - - +
45D ILE 3.7 0.2 - - - -
46D ASN* 2.8 50.2 + - - +
47D SER* 3.0 31.9 + - - +
60D VAL* 1.3 72.3 - - - +
62D ILE* 1.3 66.0 + - - +
109D HIS* 3.3 19.6 + - - -
131D ARG* 3.1 24.2 + - - +
132D LEU 3.3 6.0 + - - -
133D THR* 2.9 26.7 + - + +
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Residues in contact with ILE 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D ILE* 4.3 17.5 - - + -
44D PHE 3.2 13.2 - - - +
45D ILE* 4.3 15.3 - - + -
46D ASN 4.4 0.4 - - - +
60D VAL* 3.8 23.3 - - + -
61D ASN* 1.3 80.8 - - - +
63D PHE* 1.3 71.2 + - - +
64D LEU* 4.2 14.6 - - + +
100D PHE* 4.1 17.3 - - + -
131D ARG* 3.3 5.4 - - - +
132D LEU* 2.9 46.7 + - + +
134D LEU* 4.0 22.2 - - + -
154D MET* 4.5 9.0 - - + -
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Residues in contact with PHE 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C PHE* 4.2 13.7 - + - -
101C ALA* 6.3 0.4 - - + -
157C GLU* 4.8 0.2 - - - -
159C PHE* 3.7 29.2 - + - -
202C TYR* 3.6 39.5 - + - -
43D ILE* 3.3 6.6 - - - +
44D PHE* 2.9 44.0 + + + -
46D ASN* 4.7 18.4 - - - -
61D ASN* 4.7 0.2 - - - -
62D ILE* 1.3 80.7 - - - +
64D LEU* 1.3 60.1 + - - +
65D ARG* 3.7 32.8 - - - +
129D SER* 3.9 7.0 - - - +
130D ILE 3.5 4.3 - - - +
131D ARG* 3.8 26.2 - - + -
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Residues in contact with LEU 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D CYS* 5.0 2.5 - - + -
42D ASN 4.0 2.2 - - - +
43D ILE* 4.0 20.6 - - + -
62D ILE* 3.9 13.2 - - + -
63D PHE* 1.3 71.5 - - - +
65D ARG* 1.3 67.1 + - - +
66D GLN* 3.9 24.6 + - + +
98D LEU* 3.8 27.6 - - + -
100D PHE* 4.1 11.2 - - + -
128D TYR 3.5 2.1 - - - +
129D SER* 3.2 3.8 - - - -
130D ILE* 2.8 48.2 + - + +
132D LEU* 4.2 11.7 - - + -
156D LEU* 4.0 20.9 - - + -
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Residues in contact with ARG 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C TYR* 3.6 25.5 - - - +
203C ASN* 3.3 15.6 + - - -
204C THR* 3.8 15.1 + - + +
40D THR 3.7 0.4 - - - +
41D CYS* 3.3 8.0 - - - +
42D ASN* 2.7 81.9 + - - +
44D PHE* 3.7 24.7 - - - +
63D PHE* 3.7 20.7 - - - +
64D LEU* 1.3 75.9 - - - +
66D GLN* 1.3 64.8 + - - +
67D LYS* 5.4 0.4 - - - -
127D LEU* 4.2 17.0 - - + -
128D TYR 3.4 3.4 - - - +
129D SER* 3.2 29.0 + - - +
177D GLN* 2.9 19.0 + - - -
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Residues in contact with GLN 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D VAL* 4.1 10.7 - - + +
40D THR 3.4 2.7 - - - -
41D CYS* 4.3 9.4 - - - -
64D LEU* 3.9 21.2 - - + +
65D ARG* 1.3 78.6 - - - +
67D LYS* 1.3 63.0 + - - +
68D TRP* 3.8 18.0 - - + -
96D PRO* 3.4 33.3 + - - +
98D LEU* 3.8 26.8 - - + +
126D VAL 3.8 0.3 - - - +
127D LEU* 3.6 3.1 - - - +
128D TYR* 2.8 60.9 + - - +
130D ILE* 5.3 1.8 - - - +
168D PHE* 4.9 0.2 - - - -
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Residues in contact with LYS 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C ASN* 5.9 4.4 + - - -
38D GLN 3.7 0.9 - - - +
39D VAL* 3.3 2.4 - - - -
40D THR* 2.8 49.8 + - + +
42D ASN* 4.1 8.7 - - - +
65D ARG* 5.4 0.9 - - - -
66D GLN* 1.3 80.5 - - - +
68D TRP* 1.3 67.1 + - - +
126D VAL 3.3 11.2 - - - +
127D LEU* 4.0 26.9 - - + -
171D GLN* 2.8 31.5 + - - +
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Residues in contact with TRP 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D PRO* 4.3 2.5 - - + -
37D VAL* 4.0 10.5 - - + -
38D GLN 3.6 16.6 - - - +
39D VAL* 4.2 4.9 - - + -
66D GLN* 3.8 25.4 - - + -
67D LYS* 1.3 85.9 - - - +
69D ASN* 1.3 72.6 + - - +
70D ASP* 4.3 7.2 + - - +
93D ILE* 4.6 4.5 - - + -
94D TRP* 3.5 48.1 + + - -
95D LYS* 3.9 8.5 - - + -
96D PRO* 3.6 31.2 - - + -
125D ASN* 3.4 5.6 - - - +
126D VAL* 2.7 67.9 + - + +
128D TYR* 3.8 15.7 - + + -
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Residues in contact with ASN 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D PRO* 3.4 19.2 - - - +
31D ASN* 4.9 5.0 + - - +
37D VAL* 4.9 3.9 - - - +
38D GLN 4.7 2.0 + - - -
68D TRP* 1.3 77.8 - - - +
70D ASP* 1.3 59.6 + - - +
71D PRO* 3.3 25.5 - - - +
123D ASN* 3.0 29.4 + - - +
124D GLY 3.3 1.5 - - - -
125D ASN* 2.9 30.4 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il